3G6H

Src Thr338Ile inhibited in the DFG-Asp-Out conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations

Seeliger, M.A.Ranjitkar, P.Kasap, C.Shan, Y.Shaw, D.E.Shah, N.P.Kuriyan, J.Maly, D.J.

(2009) Cancer Res. 69: 2384-2392

  • DOI: 10.1158/0008-5472.CAN-08-3953
  • Primary Citation of Related Structures:  3G6G

  • PubMed Abstract: 
  • Imatinib is an inhibitor of the Abl tyrosine kinase domain that is effective in the treatment of chronic myelogenic leukemia. Although imatinib binds tightly to the Abl kinase domain, its affinity for the closely related kinase domain of c-Src is at ...

    Imatinib is an inhibitor of the Abl tyrosine kinase domain that is effective in the treatment of chronic myelogenic leukemia. Although imatinib binds tightly to the Abl kinase domain, its affinity for the closely related kinase domain of c-Src is at least 2,000-fold lower. Imatinib recognition requires a specific inactive conformation of the kinase domain, in which a conserved Asp-Phe-Gly (DFG) motif is flipped with respect to the active conformation. The inability of c-Src to readily adopt this flipped DFG conformation was thought to underlie the selectivity of imatinib for Abl over c-Src. Here, we present a series of inhibitors (DSA compounds) that are based on the core scaffold of imatinib but which bind with equally high potency to c-Src and Abl. The DSA compounds bind to c-Src in the DFG-flipped conformation, as confirmed by crystal structures and kinetic analysis. The origin of the high affinity of these compounds for c-Src is suggested by the fact that they also inhibit clinically relevant Abl variants bearing mutations in a structural element, the P-loop, that normally interacts with the phosphate groups of ATP but is folded over a substructure of imatinib in Abl. Importantly, several of the DSA compounds block the growth of Ba/F3 cells harboring imatinib-resistant BCR-ABL mutants, including the Thr315Ile "gatekeeper" mutation, but do not suppress the growth of parental Ba/F3 cells.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkely, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusGene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Go to Gene View: SRC
Go to UniProtKB:  P00523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6H
Query on G6H

Download SDF File 
Download CCD File 
B
N-{4-methyl-3-[(3-{4-[(3,4,5-trimethoxyphenyl)amino]-1,3,5-triazin-2-yl}pyridin-2-yl)amino]phenyl}-3-(trifluoromethyl)benzamide
C32 H28 F3 N7 O4
SNOVXGXKOHJZJH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G6HIC50: 4.6 nM BINDINGMOAD
G6HIC50: 6.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.225 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.938α = 100.99
b = 63.344β = 89.39
c = 74.179γ = 90.20
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance